Origin IGS: acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gacagcagagagcggaatttccgctctttttgtatccctttcttttttaggaaaaattgggaacaaatagaggaagattttgtgtatttgtgataaaatagaagt Mask Tandem Repeat Region ================================================ acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Find is-nt database================================================ Query_seq: SSA_1484:SSA_1485|SSA_1484:SSA_1485:DNA ligase, putative:Citrulline cluster-linked gene, putative:<-<-:1492279..1492383 105 acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1484:SSA_1485|SSA_1484:SSA_1485:DNA ligase, putative:Citrulline cluster-linked gene, putative:<-<-:1492279..1492383 105 acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1484:SSA_1485|SSA_1484:SSA_1485:DNA ligase, putative:Citrulline cluster-linked gene, putative:<-<-:1492279..1492383 105 acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 7 End: 105 ...... M L S Q I H K I F L Y L F P I F P K K E R D T K R A E I P L S A V acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1484:SSA_1485|SSA_1484:SSA_1485:DNA ligase, putative:Citrulline cluster-linked gene, putative:<-<-:1492279..1492383 105 acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_009009_SSA_1484_SSA_1485|DNA ligase, putative:Citrulline cluster-linked gene, putative|NEGATIVE:NEGATIVE|[1492279,1492383]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc acttctattttatcacaaatacacaaaatcttcctctatttgttcccaatttttcctaaaaaagaaagggatacaaaaagagcggaaattccgctctctgctgtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCUAUUUUAUCACAAAUACACAAAAUCUUCCUCUAUUUGUUCCCAAUUUUUCCUAAAAAAGAAAGGGAUACAAAAAGAGCGGAAAUUCCGCUCUCUGCUGUC ....................(((((.............(((((((((..(((((......)))))..)))).))))).(((((((.....))))))).)).))). (-21.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAGCAGAGAGCGGAAUUUCCGCUCUUUUUGUAUCCCUUUCUUUUUUAGGAAAAAUUGGGAACAAAUAGAGGAAGAUUUUGUGUAUUUGUGAUAAAAUAGAAGU .((((.(((((((((.....))))))))))))).((((((((((....))))))....))))(((((((.(.((.....)).).))))))).............. (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 840 100 51 191 142 NC_009009:SSA_1484|5end_DNA_ligase,_putative_1492188..1492418_NEGATIVE 359 100 51 69 18 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 359 100 51 204 153 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 235 57 20 204 171 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 233 99 55 230 189 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 227 60 29 130 102 NC_009009:SSA_1846|5end_Phosphoprotein_phosphatase,_putative_1840918..1841148_NEGATIVE 227 99 59 170 134 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 222 100 82 229 210 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 220 95 58 53 16 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 220 98 69 196 165 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 220 85 49 193 151 NC_009009:SSA_0380|5end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_370916..371146_POSITIVE 219 56 30 61 26 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 219 99 71 225 192 NC_009009:SSA_0139|5end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134183..134413_POSITIVE 218 68 29 135 92 NC_009009:SSA_1970|5end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1966915..1967145_NEGATIVE 218 99 55 99 49 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 216 95 54 152 111 NC_009009:SSA_2291|5end_hypothetical_protein_2293204..2293434_POSITIVE 215 47 2 151 96 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 215 100 69 186 156 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 213 48 30 149 128 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 212 70 29 139 99 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 100 51 69 18 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 249 97 62 54 10 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 245 88 46 76 18 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 244 95 61 99 59 NC_009009:SSA_0883|3end_Glycerate_kinase,_putative_878758..878908_POSITIVE 235 57 20 125 92 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 227 60 29 111 83 NC_009009:SSA_1847|3end_RRNA_methyltransferase_RsmB,_putative_1840937..1841087_NEGATIVE 226 69 33 145 114 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 226 97 52 83 41 NC_009009:SSA_0027|3end_Acyl_carrier_protein,_putative_31802..31952_POSITIVE 219 99 71 77 44 NC_009009:SSA_0138|3end_Metal-binding_(Zn)_permease,_putative_134115..134265_POSITIVE 218 99 55 102 52 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 216 98 51 51 14 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 215 47 2 151 96 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 213 48 30 138 117 NC_009009:SSA_1568|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571960..1572110_POSITIVE 213 99 67 86 46 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 212 70 29 54 14 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 211 97 75 81 56 NC_009009:SSA_1616|3end_PhoH-like_protein,_putative_1619356..1619506_NEGATIVE 209 99 52 73 2 NC_009009:SSA_0747|3end_DD-carboxypeptidase,_putative_729371..729521_POSITIVE 206 100 52 101 35 NC_009009:SSA_0799|3end_hypothetical_protein_781713..781863_NEGATIVE 206 95 62 70 32 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 204 56 30 151 111 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE